During the reign of King Joseph (José) I of Portugal, following the devastating 1755 earthquake, the library underwent a significant transformation. In an effort to rebuild and replenish the collections, acquisitions were made from prominent noble houses, securing an impressive array of materials. However, the library's fate took an unexpected turn when the royal family departed for Brazil during the Napoleonic era. The library, along with the Crown's manuscripts, found its temporary home in Rio de Janeiro. Yet, upon King Dom João VI's return to Portugal in 1821, only the manuscripts accompanied him, while the remaining volumes in Rio de Janeiro became the foundation of what is now known as the National Library of Brazil.

Unfortunately, records documenting the library's inception have been lost to time. Apart from a set of internal regulations from the 17th century, there are limited documents governing its operations. Nevertheless, successive monarchs, including King Dom João VI and King Dom Miguel, played a pivotal role in reestablishing the library. They implemented a legal deposit system, granting the library responsibility for archives and library functions. This complemented the work of the Royal Press, enhancing the institution's significance. Until the Proclamation of the Republic, the library enjoyed a privileged position, directly administered by the Royal Household and subject to the personal authority of the monarch. The appointment of librarians rested with the sovereign, often selecting individuals who held their trust, such as Alexandre Herculano, Magalhães Coutinho, and Ramalho Ortigão.

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Over time, the library's collection expanded through the integration of private libraries, including those belonging to renowned individuals and abolished religious orders. Documentation from public institutions, particularly the Ministry of the Kingdom, further enriched the holdings. Private libraries of notable figures such as Dr. Nicolau Francisco Xavier da Silva, the Count of Redondo, Barbosa Machado, and Kings Dom Pedro V, Dom Luís, and Dom Carlos, were incorporated into the library. Additionally, catalogs from other libraries provide evidence of their integration into the broader collection, including those of Carlota Joaquina of Spain, Queen of Portugal, Princess Dona Maria Francisca Benedita, and various Jesuit institutions.

The Ajuda Library stands today as a testament to the perseverance and dedication of generations of librarians, monarchs, and benefactors who have contributed to its development. Its rich and diverse holdings, accumulated through careful curation and strategic acquisitions, serve as a valuable resource for scholars, researchers, and bibliophiles alike. The library's journey, shaped by historical circumstances and the passion for knowledge, continues to inspire and enlighten visitors from around the world.